Long intergenic non-coding RNA expression signature in human breast cancer.
Long intergenic non-coding RNA expression signature in human breast cancer.
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DOI：
10.1038/srep37821
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发表时间：
2016-11-29
影响因子：
4.6
通讯作者：
Long J
中科院分区：
文献类型：
--
作者：
Zhang Y;Wagner EK;Guo X;May I;Cai Q;Zheng W;He C;Long J
乳腺癌是一种复杂的疾病，其特点是基因失控。较少系统研究长基因间非编码RNA(LincRNAs)作为乳腺癌发病机制的生物标志物或包括受体状态和患者生存在内的几个临床病理变量的能力。我们设计了两个阶段的研究，包括来自癌症基因组图谱(TCGA)的1000个乳腺肿瘤RNA-SEQ数据作为发现阶段，50例乳腺癌患者匹配的肿瘤和邻近正常组织的RNA-SEQ数据作为复制阶段，以及23例健康女性正常乳腺组织的RNA-SEQ数据作为复制阶段。我们识别了83个在乳腺肿瘤中有显著表达变化的lincRNA，发现数据集中的 <； 的错误发现率为1%。83个中的37个在复制数据集中进行了验证。整合基因组分析表明，这37个lincRNAs的异常表达可能与几种转录因子的表达变化有关。我们观察到lincRNAs及其邻近基因之间的差异共表达模式。我们发现，一种lincRNA(Rp5-1198O20，EnSembl ID ENSG00000230615)的表达水平与P <； 0.05的乳腺癌生存率相关。我们的研究确定了一组在乳腺癌中异常表达的lincRNA。
Breast cancer is a complex disease, characterized by gene deregulation. There is less systematic investigation of the capacity of long intergenic non-coding RNAs (lincRNAs) as biomarkers associated with breast cancer pathogenesis or several clinicopathological variables including receptor status and patient survival. We designed a two-stage study, including 1,000 breast tumor RNA-seq data from The Cancer Genome Atlas (TCGA) as the discovery stage, and RNA-seq data of matched tumor and adjacent normal tissue from 50 breast cancer patients as well as 23 normal breast tissue from healthy women as the replication stage. We identified 83 lincRNAs showing the significant expression changes in breast tumors with a false discovery rate (FDR) < 1% in the discovery dataset. Thirty-seven out of the 83 were validated in the replication dataset. Integrative genomic analyses suggested that the aberrant expression of these 37 lincRNAs was probably related with the expression alteration of several transcription factors (TFs). We observed a differential co-expression pattern between lincRNAs and their neighboring genes. We found that the expression levels of one lincRNA (RP5-1198O20 with Ensembl ID ENSG00000230615) were associated with breast cancer survival with P < 0.05. Our study identifies a set of aberrantly expressed lincRNAs in breast cancer.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
30.5
作者：
通讯作者：
--
DOI：
10.1126/science.1240925
发表时间：
2013-08-16
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Carpenter S;Aiello D;Atianand MK;Ricci EP;Gandhi P;Hall LL;Byron M;Monks B;Henry-Bezy M;Lawrence JB;O'Neill LA;Moore MJ;Caffrey DR;Fitzgerald KA
通讯作者：
Fitzgerald KA
影响因子：
10.5
作者：
Cabili, Moran N.;Trapnell, Cole;Rinn, John L.
通讯作者：
Rinn, John L.